I encountered the same problem three days ago, after having ran LimeWire 2.8.6 Pro on my Windows XP Dell Dimension for some time without any problems. I became aware of this issue when some, but not all, of the files I was downloading during a particular session ended up in the wrong folder. Every attempt at restoring my previous Save Directory - which I have been using for 15 months - were futile. Removing and re-installing the software did not solve the issue, nor did shutting off the Cookie controls of my ZoneAlarm Pro firewall.

I just e-mailed LimeWire Support to inquire about this issue. As soon as I am informed of a fix, I will share its details here.